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Changed SPRINT shortcut so that you can use both the new syntax for t…
…his action and the old one
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Gareth Aneurin Tribello
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Gareth Aneurin Tribello
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| /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ||
| Copyright (c) 2013-2020 The plumed team | ||
| (see the PEOPLE file at the root of the distribution for a list of names) | ||
| See http://www.plumed.org for more information. | ||
| This file is part of plumed, version 2. | ||
| plumed is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU Lesser General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
| plumed is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU Lesser General Public License for more details. | ||
| You should have received a copy of the GNU Lesser General Public License | ||
| along with plumed. If not, see <http://www.gnu.org/licenses/>. | ||
| +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ | ||
| #include "core/ActionShortcut.h" | ||
| #include "core/ActionRegister.h" | ||
| #include "core/PlumedMain.h" | ||
| #include "core/ActionSet.h" | ||
| #include "core/Group.h" | ||
|
|
||
| //+PLUMEDOC MATRIX CONTACT_MATRIX | ||
| /* | ||
| Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. | ||
| As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the | ||
| so called adjacency matrix. An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether | ||
| or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not. These matrices can then be further | ||
| analyzed using a number of other algorithms as is detailed in \cite tribello-clustering. | ||
| For this action the elements of the contact matrix are calculated using: | ||
| \f[ | ||
| a_{ij} = \sigma( |\mathbf{r}_{ij}| ) | ||
| \f] | ||
| where \f$|\mathbf{r}_{ij}|\f$ is the magnitude of the vector connecting atoms \f$i\f$ and \f$j\f$ and where \f$\sigma\f$ is a \ref switchingfunction. | ||
| \par Examples | ||
| The input shown below calculates a \f$6 \times 6\f$ matrix whose elements are equal to one if atom \f$i\f$ and atom \f$j\f$ are within 0.3 nm | ||
| of each other and which is zero otherwise. The columns in this matrix are then summed so as to give the coordination number for each atom. | ||
| The final quantity output in the colvar file is thus the average coordination number. | ||
| \plumedfile | ||
| mat: CONTACT_MATRIX ATOMS=1-6 SWITCH={EXP D_0=0.2 R_0=0.1 D_MAX=0.66} | ||
| COLUMNSUMS MATRIX=mat MEAN LABEL=csums | ||
| PRINT ARG=csums.* FILE=colvar | ||
| \endplumedfile | ||
| */ | ||
| //+ENDPLUMEDOC | ||
|
|
||
| namespace PLMD { | ||
| namespace adjmat { | ||
|
|
||
| class ContactMatrixShortcut : public ActionShortcut { | ||
| public: | ||
| static void registerKeywords(Keywords& keys); | ||
| explicit ContactMatrixShortcut(const ActionOptions&); | ||
| }; | ||
|
|
||
| PLUMED_REGISTER_ACTION(ContactMatrixShortcut,"CONTACT_MATRIX") | ||
|
|
||
| void ContactMatrixShortcut::registerKeywords(Keywords& keys) { | ||
| ActionShortcut::registerKeywords( keys ); | ||
| keys.add("atoms","GROUPA",""); | ||
| keys.add("atoms","GROUPB",""); | ||
| keys.add("atoms-2","ATOMS","the atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)"); | ||
| keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable"); | ||
| keys.add("compulsory","NN","6","The n parameter of the switching function "); | ||
| keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); | ||
| keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); | ||
| keys.add("compulsory","R_0","The r_0 parameter of the switching function"); | ||
| keys.add("numbered","SWITCH","specify the switching function to use between two sets of indistinguishable atoms"); | ||
| keys.add("compulsory","NL_CUTOFF","0.0","The cutoff for the neighbor list. A value of 0 means we are not using a neighbor list"); | ||
| keys.add("compulsory","NL_STRIDE","1","The frequency with which we are updating the atoms in the neighbor list"); | ||
| keys.addFlag("COMPONENTS",false,"also calculate the components of the vector connecting the atoms in the contact matrix"); | ||
| keys.addFlag("NOPBC",false,"don't use pbc"); | ||
| keys.addActionNameSuffix("_PROPER"); keys.needsAction("TRANSPOSE"); keys.needsAction("CONCATENATE"); | ||
| } | ||
|
|
||
| ContactMatrixShortcut::ContactMatrixShortcut(const ActionOptions& ao): | ||
| Action(ao), | ||
| ActionShortcut(ao) | ||
| { | ||
| std::vector<std::string> grp_str; std::string atomsstr=""; | ||
| std::vector<std::string> atomsvec; parseVector("ATOMS",atomsvec); | ||
| if( atomsvec.size()>0 ) { | ||
| for(unsigned i=0; i<atomsvec.size(); ++i) { | ||
| Group* gg = plumed.getActionSet().selectWithLabel<Group*>( atomsvec[i] ); | ||
| if( gg ) grp_str.push_back( atomsvec[i] ); | ||
| } | ||
| if( grp_str.size()!=atomsvec.size() ) { | ||
| grp_str.resize(0); | ||
| atomsstr = " ATOMS=" + atomsvec[0]; for(unsigned i=1; i<atomsvec.size(); ++i) atomsstr += "," + atomsvec[i]; | ||
| } | ||
| } else { | ||
| std::string grp_inpt; | ||
| for(unsigned i=1;; ++i) { | ||
| if( !parseNumbered("GROUP",i,grp_inpt) ) break; | ||
| grp_str.push_back( grp_inpt ); | ||
| } | ||
| } | ||
| if( grp_str.size()>9 ) error("cannot handle more than 9 groups"); | ||
| if( grp_str.size()==0 ) { readInputLine( getShortcutLabel() + ": CONTACT_MATRIX_PROPER " + atomsstr + " " + convertInputLineToString() ); return; } | ||
|
|
||
| for(unsigned i=0; i<grp_str.size(); ++i) { | ||
| std::string sw_str, num; Tools::convert( i+1, num ); parseNumbered("SWITCH", (i+1)*10 + 1 + i, sw_str ); | ||
| if( sw_str.length()==0 ) error("missing SWITCH" + num + num + " keyword"); | ||
| readInputLine( getShortcutLabel() + num + num + ": CONTACT_MATRIX_PROPER GROUP=" + grp_str[i] + " SWITCH={" + sw_str + "}" ); | ||
| for(unsigned j=0; j<i; ++j) { | ||
| std::string sw_str2, jnum; Tools::convert( j+1, jnum ); parseNumbered("SWITCH", (j+1)*10 + 1 + i, sw_str2); | ||
| if( sw_str2.length()==0 ) error("missing SWITCH" + jnum + num + " keyword"); | ||
| readInputLine( getShortcutLabel() + jnum + num + ": CONTACT_MATRIX_PROPER GROUPA=" + grp_str[j] + " GROUPB=" + grp_str[i] + " SWITCH={" + sw_str2 +"}"); | ||
| readInputLine( getShortcutLabel() + num + jnum + ": TRANSPOSE ARG=" + getShortcutLabel() + jnum + num ); | ||
| } | ||
| } | ||
| std::string join_matrices = getShortcutLabel() + ": CONCATENATE"; | ||
| for(unsigned i=0; i<grp_str.size(); ++i) { | ||
| std::string inum; Tools::convert(i+1,inum); | ||
| for(unsigned j=0; j<grp_str.size(); ++j) { | ||
| std::string jnum; Tools::convert(j+1,jnum); | ||
| if( i>j ) join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum + jnum; | ||
| else join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum + jnum; | ||
| } | ||
| } | ||
| readInputLine( join_matrices ); | ||
| } | ||
|
|
||
| } | ||
| } |
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